Re: Another question on Diffusion

From: Neelanjana Sengupta (
Date: Wed Nov 08 2006 - 15:58:09 CST

Since your system is in a bilayer, it should be fine. Had it been in a
solvent like water, you could have considered not doing wrapAll.

On 11/8/06, Vinit Rege <> wrote:
> I was reading some of the posts here and I am not confused a bit about
> using WrapAll in the simulations. I am running MD on a system of
> bacteriorhodopsin in POPC bilayer with PBC and wrapall set ON... I am trying
> to get RMSD plot and eventually Diffusion coefficients... Am I being wrong
> to use WrapAll ?
> sincerely,
> Vinit

Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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